Following an apprenticeship as bank teller he worked at a bank in Lübbecke before being made redundant. After having been unemployed for two and a half years, he joined the SS in October 1933 and the Nazi Party in May 1937.

On 16 November 1939 he joined the 9th SS Infantry Regiment based at Danzig and, in 1940, became the adjutant to the commanding SS officer of the Neuengamme concentration camp, Martin Gottfried Weiss. In 1942 Weiss was also the commanding officer of the Arbeitsdorf concentration camp with Höcker serving as his adjutant. Before being transferred in May 1943 to the Majdanek concentration camp, again as adjutant to Weiss, Höcker followed a course at the SS military academy (Junkerschule) in Braunschweig. During the same period he also received some military training.

In 1943, he became the adjutant to the commandant at Majdanek during the Operation Reinhardt mass deportations and murders. Afterward, he became adjunct to Richard Baer, in 1944, who was previously deputy to WVHA chief Oswald Pohl in Berlin. In May 1944 Höcker was transferred to Auschwitz, where he remained until the advance of the Soviet Red Army forced camp evacuation in January 1945. Thereafter, he was transferred to the Dora-Mittelbau concentration camp along with Baer. The two men administered the camp until the Allies arrived. Höcker used false papers to flee the camp and avoid being identified by the British when they captured him.

He married before the war and had a son and daughter during the war, with whom he was reunited after his release from 18 months in a British POW camp in 1946. Early in the 1960s he was apprehended by West German authorities in his hometown, where he was a bank official. It is not known why the bank rehired and promoted him after a long absence.

At his trial in Frankfurt, part of the noted Frankfurt Auschwitz Trials, Höcker denied having participated in the selection of victims at Birkenau or having ever personally executed a prisoner. He further denied any knowledge of the fate of the approximately 400,000 Hungarian Jews who were murdered at Auschwitz during his term of service at the camp. Höcker was shown to have knowledge of the genocidal activities at the camp, but could not be proved to have played a direct part in them. In post-war trials, Höcker denied his involvement in the selection process. While accounts from survivors and other SS officers all but placed him there, prosecutors could locate no conclusive evidence to prove the claim.

In August 1965 Höcker was sentenced to seven years imprisonment for aiding and abetting in over 1,000 murders at Auschwitz. He was released in 1970 and was able to return to his bank post as a chief cashier, where he worked until his retirement.

On 3 May 1989 a district court in the Germany city of Bielefeld sentenced Höcker to four years imprisonment for his involvement in gassing to death prisoners, primarily Polish Jews, in the concentration camp Majdanek in Poland. Camp records showed that between May 1943 and May 1944 Höcker had acquired at least 3,610 kilograms of Zyklon B poisonous gas for use in Majdanek from the Hamburg firm of Tesch & Stabenow.[1]

Höcker died in 2000, still claiming that he had nothing to do with the death camp at Birkenau. During his final statement at the Frankfurt Trial in 1965, he had claimed, “I only learned about the events in Birkenau…in the course of time I was there… and I had nothing to do with that. I had no ability to influence these events in any way…neither did I want them, nor carry them out. I didn’t hurt anybody… and neither did any one die at Auschwitz because of me.”
Höcker testified that he never set foot on the ramp during the selection process, despite one survivor recalling an officer with the surname Höcker being present on the ramp.

A documentary airing on The National Geographic Channel, "Scrapbook from Nazi Hell", examined the claims made by former prisoners at Auschwitz that there was a German officer with the surname Höcker present on the ramp during the selection process. Photographic analysts used data gained from measurements of Höcker in the several photographs in his album. Measurements from photogrammetric analysis, along with the height listed in his SS service records, were compared to a figure found in two of the photos from the "Auschwitz Album" (made by SS photographers) whose face cannot be seen. The SS-Oberscharführer, whose face cannot be seen because his back is facing the camera, is shown on the ramp where the new arrivals disembarked from the trains and went through the "selection" process (the sorting of prisoners healthy enough to be useful as forced labor, in contrast with the sick, the elderly, women with small children, and children, who were sent immediately to the gas chambers). It is significant to note that during his trial and for the rest of his life, Karl Höcker vehemently denied that he had anything to do with killing, and was never present or participated in the selection process. The results of the measurements gleaned from the "Höcker Album" showed that there was almost an exact match to the SS-Oberscharführer shown on the ramp during selection, though barring definitive eyewitness testimony, it is nearly impossible to prove beyond a reasonable doubt that the man in the photo is indeed Höcker. The FBI Photographic Analyst who consulted on the measurements taken from the photos believes that there is enough evidence to say that the man is most likely Höcker. There is, however, one significant discrepancy between Höcker and the Nazi on the ramp. Karl Höcker, in May 1944 upon his appointment as Adjutant to the Camp Commandant, held the rank of SS-Obersturmfürher (first lieutenant), yet the unknown SS-Oberscharführer (technical sergeant) uniform insignia does not match that rank. As a possible explanation for this, it was posited by the documentary that Höcker may have worn the uniform of lower ranking to conceal his true identity. Barring concrete evidence, all the above is conjecture.